tbuckley/cabot-search huggingface dataset:
IMMU-09. IMMUNOLOGICAL CHARACTERIZATION OF PEDIATRIC BRAIN TUMORS HAS CLINICAL IMPLICATIONS FOR PATIENT MANAGEMENT AND PROGNOSIS
Authors: Adrian Levine, Liana Nobre, Scott Milos, Anirban Das, Monique Johnson, Ben Laxer, Scott Ryall, Robert Siddaway, Uri Tabori, Cynthia Hawkins
Journal: Neuro-Oncology (2022)

Abstract The tumor immune microenvironment (TIME) is a growing area of interest, however, the extent of immune activation in childhood CNS tumors is unknown. Although immunotherapy has not gained success in most CNS cancers, our group described gliomas with MMRD which exhibit hypermutation and favorable responses to immune checkpoint inhibition (ICI). Therefore, detailed characterization of the CNS TIME is key for the development of novel immunotherapeutic strategies and application of existing ones in childhood brain tumors. We developed a clinical NanoString immune-oncology panel that includes markers reflecting cell types, therapeutic targets, and cellular pathways, as well as the 18-gene tumor inflammation signature (TIS), a biomarker for ICI response. We tested over 500 brain tumors, including 266 low-grade gliomas (LGG), 170 high-grade gliomas (HGG), 91 MMRD tumors, 16 ependymomas, 46 medulloblastomas, and 36 non-tumor brain samples. Overall, ependymomas and medulloblastomas had low levels of inflammation, although SHH medulloblastomas had higher inflammation than other subtypes. IDH-mutant LGG were immunologically cold, while many gliomas with pediatric-LGG mutations had high levels of inflammation, including upregulation of immune checkpoints – indicating that ICI may be an effective strategy. Interestingly, in pediatric-LGG inflammation impacted outcome in tumors with the same genetic alterations. BRAF V600E-mutant LGG exhibiting high TIS had inferior prognosis (p = 0.02), while no such relationship was observed in BRAF-fused tumors. Diffuse midline gliomas had higher inflammation than hemispheric HGG, indicating that these tumors are not immunologically cold, as has been previously reported. In MMRD tumors treated with ICI, high TIS correlated with improved survival and was independent from hypermutation and mutational burden. Furthermore, MMRD gliomas had high expression of several other immune checkpoints including LAG3, suggesting its value as an additional therapeutic target. In summary, characterization of the TIME across pediatric brain tumors provides potential prognostic clues and suggest treatment strategies for further investigation.
BIOM-34. MULTIPLEX PHENOTYPING OF EXTRACELLULAR VESICLES FOR ANALYSIS OF POTENTIAL BIOMARKERS IN GLIOBLASTOMA PATIENTS
Authors: Amanda Salviano-Silva, Kathrin Wollmann, Cecile Maire, Katharina Kolbe, Lasse Dührsen, Katrin Lamszus, Franz Ricklefs
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION Extracellular vesicles (EVs) carry biological information from their cell of origin that is useful for non-invasive detection of tumor biomarkers and disease monitoring. In glioblastoma (GBM), blood circulating EVs are elevated and carry GBM-associated proteins. However, it is still challenging to analyze tumor derived EVs for translational purposes. Here, we used imaging flow cytometry (IFCM) as a robust strategy to perform phenotyping of EVs with GBM related surface markers in human plasma. METHODS EVs were isolated via differential ultracentrifugation from plasma of (a) 40 GBM patients, pre- and post-surgery, (b) 11matched GBM relapses and (c) 12 healthy donors (HD). EV sizes and concentrations were evaluated by NTA. EV markers (CD9,CD63 and CD81) together with glioma-related markers (integrin beta-1 [ITGB1], tenascin C [TNC], Profilin-1 [PFN1], CD44,GPNMB, SPARC, HLA-II or CD133) were analyzed by IFCM. EV percentages and objects/mL plasma were compared among the groups and correlated with clinical parameters. RESULTS CD9 was the predominant tetraspanin in all groups (15-96%), while CD63 had the lowest levels (0-33%) and the strongestdecrease in GBM patients after surgery (fold change [FC]=-5.4, p&amp;lt;0.01). Among the glioma-related markers, ITGB1 and TNC displayed the most significant differences between the analyzed groups, especially the double positives ITGB1+/CD63+and TNC+/CD63+, which decreased in patients after tumor removal (FC=-3.5 and -12, respectively; p&amp;lt;0.001). Meanwhile,ITGB1+/CD9+and TNC+/CD9+EVs exhibited the highest levels in GBM when compared to HD subjects (FC=8.6 and 17.4;p&amp;lt;0.001) and upon tumor recurrence (FC=3.7 and 10.9, respectively; p&amp;lt;0.01). SUMMARY/CONCLUSION We identified EV surface antigens with potential clinical utility as GBM biomarkers. Among them, we highlight ITGB1 and TNC as the most promising markers.
EPID-01. PROFILE AND OUTCOME OF PATIENTS WITH BRAIN METASTASES IN YOGYAKARTA, INDONESIA
Authors: Rusdy Malueka, Rachmat Hartanto, Nurhuda Setyawan, Alfian Rismawan, Kusumo Dananjoyo, Endro Basuki, Ahmad Asmedi, Ery Dwianingsih
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Metastatic brain tumors cause significant morbidity and mortality and often have a poor prognosis. Currently, there are limited epidemiology data on metastatic brain tumors in Indonesia. This study aimed to identify demographic, clinical characteristics, and outcomes of patients with brain metastases in Yogyakarta Province, Indonesia. METHODS Demographic and clinicopathological data were collected from medical records of brain tumor patients admitted to six major hospitals in Yogyakarta Province, Indonesia, for five years (2015–2019). RESULTS In total, 395 patients were included. Most patients were females (254, 64.3%). The mean age of the patients was 51.6±15.0 years old. Headache was the most common presenting symptom (53.2%), followed by a motoric deficit (48.4%), cognitive impairment (24.3%), loss of consciousness (21.3%), and a seizure (20.8%). The most common primary tumors that metastasize to the brain were lung (36.6%) and breast cancer (32.7%). The median overall survival of patients with brain metastases was 11±2.36 months. CONCLUSION Lung and breast cancers are the most common source of brain metastases in Yogyakarta, Indonesia. Overall survival of patients with brain metastases in this area is still relatively short.
IMMU-24. TESTOSTERONE FUNCTIONS AS A TUMOR SUPPRESSOR IN GLIOBLASTOMA
Authors: Juyeun Lee, Daniel Silver, Yoon-Mi Chung, Nima Sharifi, Justin Lathia
Journal: Neuro-Oncology (2022)

Abstract A sex difference in the incidence and outcome of patients with glioblastoma (GBM), the most common primary malignant brain tumor, has been well established, as male patients experience a worse prognosis. However, the contribution of sex hormones to anti-tumor immunity has not been fully explored. To test this, we orthotopically implanted syngeneic mouse GBM cells into male mice after castration or sham surgery to assess survival differences. Castrated immune-competent mice succumbed to tumors significantly faster than the sham surgery group, and this was rescued by exogenous testosterone administration. This finding was further corroborated by that blockade of androgen signaling using enzalutamide reproduced the effect of castration with shortened survival. In contrast, castration on immunocompromised mice, NSG and RAG1KO, resulted in no survival difference compared to sham animals, suggesting a role for immune system. Flow cytometry analysis of tumor-infiltrating immune cells revealed decreased cytokine production in T and NK cells from castrated mice, while no difference was found in immune cell infiltration. Flank tumor experiments suggested brain-specific regulation of T cell recruitment, as tumor growth was delayed in castrated mice with increased infiltration of CD8+ T cell. It is noted that decreased cytokine production in T cells and NK cells was observed in tumor as well as lymph nodes from flank tumor model. Surprisingly, mass spectrometry of serum revealed upregulated levels of circulating corticosterone in castrated mice regardless of tumor presence, suggesting that castration may induce systemic immunosuppression and regulate T cell infiltration to brain via upregulation of glucocorticoids. Taken together, our data demonstrate that testosterone regulates T cell immunity, possibly via glucocorticoids, and ultimately affects GBM tumor growth. Given the decreased level of testosterone in aged males with higher risk of GBM, these findings further suggest the potential therapeutic intervention of testosterone in GBM.
DISP-09. THE GENOMIC PROFILES AND CLINICAL MANIFESTATIONS OF MENINGIOMAS VARY AMONGST DIFFERENT RACES
Authors: Shaurey Vetsa, Sagar Vasandani, Muhammad Jalal, Kanat Yalcin, Mark Youngblood, Neelan Marianayagam, Aladine Elsamadicy, Hanya Qureshi, Arushii Nadar, Mani Ratnesh Sandhu, Stephanie Aguilera, Ketu Mishra-Gorur, Declan McGuone, Robert Fulbright, Lan Jin, E Zeynep Erson-Omay, Murat Günel, Jennifer Moliterno
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND While socioeconomic factors for racial disparities amongst sporadic meningioma patients have been explored, other potential influences are poorly understood. We sought to identify whether the genomic make-up is different amongst meningioma patients of different races and how they correlate with clinical variables. METHODS All patients who underwent surgery for sporadic meningioma and consented for whole exome sequencing were eligible. Genomic and clinical data were reviewed and analyzed. RESULTS 537 intracranial meningiomas from 483 patients with the following racial profile were included: 75% White, 14% Black, 8% Latinx, 3% Asian. Compared with others, Whites were older at the time of diagnosis (p = 0.038) and surgery (p = 0.015). Black and Latinx patients were more likely to present with vision abnormalities (p = 0.006). Whites were more likely to have convexity meningiomas (p = 0.003), while Blacks were more likely to have tumors along the anterior fossa (p = 0.002) with associated somatic Hedgehog (HH) driver mutations (p = 0.008). Both Black and Latinx patients were more likely to have TRAF7 mutated meningiomas (p = 0.006). The highest number of copy number variations was seen in Blacks (p = 0.011) and this correlated with Blacks being more likely to have high-grade tumors, followed by Whites, Asians, and then Latinx (p = 0.020). Black patients trended toward decreased progression-free survival than others (median survival: 57 vs. 130 months; p = 0.06) despite similar extent of resection. CONCLUSION Overall, when mutational subgroup and location are considered, Black patients are more likely to have anterior skull base meningiomas with associated visual issues and corresponding somatic HH and TRAF7 mutations. With regards to tumor grade, Blacks harbor more aggressive sporadic meningiomas with a larger prevalence of high-grade meningiomas and associated underlying chromosomal instability compared to others. These findings have implications for meningioma care especially in minority populations, who may harbor more aggressive tumors.
DDDR-30. UNRAVELING THE NOVEL ANTI-TUMOR MECHANISM OF ST-401, A BRAIN PENETRANT MICROTUBULE TARGETING AGENT
Authors: Kainat Khan, Juan Vicente, José McFaline-Figueroa, Linda Wordeman, Nephi Stella
Journal: Neuro-Oncology (2022)

Abstract Microtubule targeting agents (MTAs) are indispensable medicines to treat a wide range of cancers. While evidence suggests that glioblastoma (GBM) is sensitive to disruptions in microtubule (MT) functions; most MTAs do not reach the brain. To address this limitation, we developed a brain-penetrant MTA, ST-401, that kills patient-derived GBM in culture at nanomolar concentrations, binds to colchicine sites through a unique interaction mode, gently and reversibly inhibits MT assembly and kills cancer cells through a novel anti-tumor mechanism as determined by analysis of its activity in the NCI 60 cancer cell panel compared to the Approved Oncology Agents library (Horne et al. (2020) Neuro-Onc Adv. 3(1): vdaa165).We used flow cytometry to confirm that nocodazole (10-100 nM) treatment of HCT116 cells triggered apoptosis, necrosis, and accumulation of autophagosomes, as well as increase in p-P53. By sharp contrast, ST-401 did not trigger these responses. Live cell imaging showed that NOC preferentially kills HCT116 cells in mitosis whereas ST-401 preferentially kills these cells in interphase. ScRNAseq analysis of NOC and ST-401 treatment of HCT-116 cells showed that ST-401 down-regulates MYC mRNA expression, suggesting that ST-401 might affect MYC function. MYC protein levels are regulated by multiple mechanisms, including phosphorylation at residue Thr58 that promotes its ubiquitination and proteasome degradation. We discovered that ST-401 increases MYC phosphorylation on Thr58 and down-regulates MYC protein expression in both HCT116 and the GBM cell line, U251.Our result suggests that the novel anti-tumor mechanism of ST-401 might involve cell death in interphase and reduced MYC expression. Funded by NIH (CA244213 to NS and NS106924 to NS).
IMMU-20. MODULATION OF THE PERIPHERAL T CELL BIOLOGY IN GLIOBLASTOMA
Authors: Malte Mohme, Alessandra Rünger, Laura Glau, Alice Ryba, Krystian Fita, Ceren Saygi, Malik Alawi, Manfred Westphal, Eva Tolosa, Cecile Maire, Katrin Lamszus
Journal: Neuro-Oncology (2022)

Abstract Cancer is a systemic disease. Due to the exceedingly rare occurrence of metastasis of cerebral glioma, systemic alterations have, however, not been considered to play a major role in disease progression of glioma. T cells orchestrate the adaptive immune response in an antigen-specific, cytokine mediated manner. The aim of our study was to investigate how cerebral glioma impacts systemic T cell immunobiology. We performed gene expression profiling of peripheral blood T cells in patients with IDHwt glioblastomas as well as in a murine glioma model. In addition, we analyzed the levels of soluble immune biomarkers in patient blood and performed flow-cytometric phenotyping of human peripheral blood CD3+ T cells. We discovered a significant skewing of peripheral T cell phenotypes in IDHwt glioblastoma patients compared to healthy donors (HD), showing CD4+ TH1 expansion and reduced numbers of T follicular helper cells (TFH), TH1* and mucosa associated invariant T (MAIT) cells, while TH2 and TH17 percentages remained stable. Interestingly, peripheral memory CD4+ T cells exhibited reduced Fas and PD-1 expression, while CD8 T cells were primarily affected in the non-memory CD45RA+ compartment, displaying reduced numbers of CD8+ CD127+ CD27+ cells. Compared to healthy individuals, GBM patients had significantly increased levels of soluble CD27 while levels of soluble CD25 were reduced (p &amp;lt; 0.05). GSEA and ORA analysis of differentially expressed genes in murine gliomas showed alterations in RNA binding and processing, as well as ribosomal activity in both cell types, indicating systemic modulation in translational- and cell cycle pathways in glioblastoma. Taken together, our results demonstrate a significant skewing of the peripheral T immunobiology in patients with IDHwt gliomas. Our data highlights the importance of considering malignant glioma as a systemic disease that fundamentally alters the immune repertoire in affected patients.
EPCO-35. THE ZINC FINGER IN THE CEREBELLUM (ZIC1/4) LOCUS IS A CONTEXT DEPENDENT DRIVER GENE IN MEDULLOBLASTOMA
Authors: John Lee, Ran Tao, Zhen You, Frank Huang, Paul Northcott, Michael Taylor
Journal: Neuro-Oncology (2022)

Abstract Medulloblastoma (MB) is a malignant paediatric brain tumor comprised of 4 molecularly and clinically distinct subgroups: WNT, SHH, Group 3 and Group 4. Previous studies have reported recurrent, mutually exclusive epigenetic modifier mutations converging in these subgroups, as well as aberrant H3K27me3 depositions within these tumors. While these observations hint at aberrant epigenetic mechanisms driving MB pathobiology, detailed understanding of MB chromatin landscape remains elusive to date. As such, chromatin landscape of MB was defined by conducting H3K27Ac ChIP-Seq in 102 primary MB tumors and H3K27me3 ChIP-Seq in 63 overlapping tumors. Chromatin landscape of Medulloblastoma was subgroup specific and H3K27me3 modification recurrently repressed ZIC1 in Group 3 and 4 MB, a driver gene that is also recurrently mutated within Group 4 and SHH MB. Validation cohort comprised of 251 MB samples with matching RNA-Seq and WGS data demonstrated that the ZIC1 - ZIC4 locus (ZIC1/4) undergoes recurrent epigenetic repression of single alleles in 25% of Group 3, 50% of Group 4 but rarely in other subgroups. Strikingly, ZIC1 mutations in the Group 4 tumors always occurred in the context of repression of the wildtype allele, revealing a recurrent convergence of genetic and epigenetic mechanisms targeting both copies of ZIC1. Overexpression of ZIC1 and ZIC4 together, or ZIC1 alone to a lesser extent, lead to reduced proliferation of Group 3 MB cells in vitro and in vivo. Intriguingly, while Group 4 ZIC1 mutations exhibited loss of function phenotypes, SHH ZIC1 mutations exhibited gain of function phenotypes. Overexpression of ZIC1 in Granule Progenitor Cells (GPC), which give rise to SHH MB, resulted in increased proliferation of cells in contrast to Group 3 MB cells. Taken together, we demonstrate that multiple epigenetic and genetic mechanisms converge to govern context dependent driver roles for ZIC1 and ZIC4 underlying MB pathobiology.
IMMU-28. THE INTRA-TUMORAL SPATIAL HETEROGENEITY OF T CELL ANTIGENS IN GLIOBLASTOMA: AN INTEGRATED MULTI-OMICS APPROACH
Authors: Gioele Medici, Marcel Wacker, Marissa Dubbelaar, Carolin Schwitalla, Friederike Hanssen, Daniel Schulz, Flavio Vasella, Elisabeth Rushing, Jens Bauer, Bernd Bodenmiller, Hans-Georg Rammensee, Luca Regli, Juliane Walz, Michael Weller, Marian Neidert
Journal: Neuro-Oncology (2022)

Abstract This study investigates the intratumoral heterogeneity of T cell antigen presentation in 15 newly diagnosed glioblastoma patients. Our multi-omics approach includes mass spectrometry-based immunopeptidome analysis, next-generation sequencing (whole-exome and RNA sequencing), and imaging mass cytometry performed on biopsies deriving from the necrotic core (NEC), the gadolinium contrast-enhancing region (T1), and the peritumoral infiltrating zone (INF, 5-ALA positive). A total of 24493 unique HLA class I and 17394 unique HLA class II peptides were identified. Comparative profiling of peptides from our study and a benign tissue database (in-house; n = 429 donors combined with HLA ligand atlas (https://hla-ligand-atlas.org)) revealed that 20% of HLA class I ligands are glioblastoma exclusive. Of these ligands, 21%, 21%, and 15% were exclusively presented in the INF, T1, or NEC zone, respectively. Here, we focused on the INF-specific antigens as this zone is likely to remain after tumor resection and gives rise to glioblastoma recurrence. Interestingly, two INF-specific HLA ligands showed a frequency presentation of 45% in our patient cohort. One ligand originated from BAALC (Brain and acute leukemia cytoplasmic protein) and one from NCAN (Neurocan core protein), which are both known to be glioblastoma-associated proteins. Immunogenicity of pre-selected candidate antigens was assessed with autologous expanded T cells and revealed a set of novel promising targets for immunotherapy. Integrated RNA/DNA sequencing also enabled the identification of neoepitopes deriving from tumor- and region-specific mutations. Furthermore, imaging mass cytometry contributed to investigating the immune compartment of the tumor microenvironment in high dimensionality and spatial resolution. In conclusion, our approach characterized the intra-tumoral regional heterogeneity of both infiltrating immune cells and tumor antigens. This multi-omics spatial atlas of the immune landscape can be used for the informed design of immunotherapy strategies against glioblastoma.
DDDR-26. IDENTIFICATION OF OLIG2 AS A PREDICTOR OF OSIMERTINIB’S EFFICACY AGAINST EGFRVIII+ GLIOBLASTOMA
Authors: Jackson Adams, Gita Kwatra, Zachary Bordeaux, Madan Kwatra
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Molecular characterization of glioblastomas by The Cancer Genome Atlas revealed molecular abnormalities in epidermal growth factor receptor (EGFR) in over 50% of glioblastomas. These included gene amplification, a large deletion in ligand binding domain (EGFRvIII), kinase duplications and gene fusions. Our laboratory has been focusing on targeting EGFRvIII in glioblastomas and we noted EGFRvIII heterogeneity. We found that growth inhibition of EGFRvIII+ glioblastoma stem cell lines D317 and D10-0171 by osimertinib was different, with D317 being more sensitive. Molecular analyses revealed that D10-0171 has 35-fold higher levels of the transcription factor OLIG2. Here we hypothesize that increased OLIG2 expression confers osimertinib resistance in EGFRvIII+ GBM. METHODS An OLIG2 knock out GSC, D10-0171 (OLIG2-KO) was generated using CRISPR. Efficacy of osimertinib in growth inhibition of D10-0171 (WT) and OLIG2-KO was examined in a subcutaneous xenograft model. Once tumors became visible, mice were treated daily with either 200 μl vehicle or 25 mg/kg osimertinib by oral gavage. RNA-seq and reverse phase protein array (RPPA) analyses were then performed on both GSC’s. RESULTS Assessment of tumor growth of both GSC’s demonstrated that OLIG2-KO cells formed tumors at a significantly lower rate than WT with a rate-based (T/C) ratio of 0.0077. Administration of osimertinib led to tumor growth inhibition in both GSCs but had a greater effect in OLIG2KO than WT, with rate-based T/C ratios of 0.099 and 0.1669, respectively. Transcriptomic analysis of OLIG2KO revealed downregulation of several pathways when compared to WT, including MYC targets V1 and V2, oxidative phosphorylation, and fatty acid metabolism, while proteomic analysis revealed downregulation of several growth-promoting pathways including ErbB and MAPK signaling. CONCLUSION Lower levels of OLIG2 increase osimertinib sensitivity of EGFRvIII+ glioblastoma. We propose a schema for selecting EGFRvIII+ patients who will respond to Osimertinib.